Genomic and Phenotypic Analysis of Multidrug-Resistant Acinetobacter baumannii Clinical Isolates Carrying Different Types of CRISPR/Cas Systems

Abstract

Acinetobacter baumannii is an opportunistic pathogen being one of the most important causative agents of a wide range of nosocomial infections associated with multidrug resistance and high mortality rate. This study presents a multiparametric and correlation analyses of clinical multidrug-resistant A. baumannii isolates using short- and long-read whole-genome sequencing, which allowed us to reveal specific characteristics of the isolates with different CRISPR/Cas systems. We also compared antibiotic resistance and virulence gene acquisition for the groups of the isolates having functional CRISPR/Cas systems, just CRISPR arrays without cas genes, and without detectable CRISPR spacers. The data include three schemes of molecular typing, phenotypic and genotypic antibiotic resistance determination, as well as phylogenetic analysis of full-length cas gene sequences, predicted prophage sequences and CRISPR array type determination. For the first time the differences between the isolates carrying Type I-F1 and Type I-F2 CRISPR/Cas systems were investigated. A. baumannii isolates with Type I-F1 system were shown to have smaller number of reliably detected CRISPR arrays, and thus they could more easily adapt to environmental conditions through acquisition of antibiotic resistance genes, while Type I-F2 A. baumannii might have stronger “immunity” and use CRISPR/Cas system to block the dissemination of these genes. In addition, virulence factors abaI, abaR, bap and bauA were overrepresented in A. baumannii isolates lacking CRISPR/Cas system. This indicates the role of CRISPR/Cas in fighting against phage infections and preventing horizontal gene transfer. We believe that the data presented will contribute to further investigations in the field of antimicrobial resistance and CRISPR/Cas studies.

The promiscuous and highly mobile resistome of Acinetobacter baumannii

“…On the one hand, because most of these isolates are within clinical settings (under constant use of antibiotics) this will select for the presence of (at least some) ARGs. On the other hand, A. baumannii has defence mechanisms, for instance CRISPR/Cas systems or restrictionmodification systems, that can impair the introduction of the mobile genetic elements harbouring the ARGs [10,11]. In this regard, a recent study has shown that a group of A. baumannii having functional CRISPR/Cas systems have considerably fewer plasmids [10].…”

“…On the other hand, A. baumannii has defence mechanisms, for instance CRISPR/Cas systems or restriction-modification systems, that can impair the introduction of the mobile genetic elements harbouring the ARGs [10, 11]. In this regard, a recent study has shown that a group of A.…”

“…Genome sequencing has also been tremendously useful to better understand the biology of A. baumannii. Studies analysing the pangenome of this species have unveiled important aspects of its genetic variation [9] and its defence mechanisms [10,11]. Additionally, population genomics and genomic surveillance studies have been very useful to study the geographical and temporal spreading of important lineages in this and other species [12][13][14][15][16][17].…”

Diversity of International High-Risk Clones of Acinetobacter baumannii Revealed in a Russian Multidisciplinary Medical Center during 2017–2019

“…The total number of isolates involved in the initial screening was 145, and 49 of them were sequenced. Earlier we have investigated the properties of the CRISPR/Cas arrays and systems for some of these isolates and a set of reference isolates from RefSeq [ 56 ]. Then we carefully selected nine isolates from the initial set, which represented the diversity of the A. baumannii international clones revealed in the hospital, and performed long-read sequencing for them.…”

CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia

“…They showed that CRISPR/Cas systems in the genomes studied contributed to phage resistance, rather than hampering the horizontal transfer of beneficial mobile genetic elements, including resistance genes. However, there are some works on Acinetobacter baumannii , Enterococcus faecalis , Streptococcus pneumoniae and Staphylococcus aureus that show the direct involvement of CRISPR/Cas systems in the interruption of the horizontal gene transfer [ 13 , 14 , 15 ]. The analysis of correlations between the CRISPR/Cas, anti-CRISPR, and antibiotic resistance gene content of more than 100,000 reference genomes of 5677 different species, including P. aeruginosa , allowed hypothesizing that the selection for antibiotic resistance could result in an accumulation of anti-CRISPR genes in the genomes that harbored both CRISPR/Cas systems and antibiotic resistance genes acquired by horizontal transfer [ 10 ].…”